I am here using the avogadro program for the construction of molecular structures, before doing DFT calculations. I use H2O and Graphene as small molecules and their substrates.
I would suggest using a Z-Matrix editing software such as Molden instead. Avogadro is nice and easy to handle but it has its limitations.
In Molden you can choose in which arrengement the coordinates relative to each other and set the exact angle.
If you need to stay in Avogadro, mark the molecule with the "cursor" function and then reorient it with the "hand" function but it may be messy to do that.
A more sophisticated approach would be to export the structure into an xyz file, open it in excel, choose e.g. the oxygen atom of the water molecule as the origin point and then use rotational and translational coordinate transformations on your graphen sheet's coordinates. Once you have figured out how to do that you will be able to work with extreme precision.
You can use this path to change the distance and angle between two molecules in Avogadro:
First, select one of a molecule with "Selection atom (a black arrow).
Second, select "Manipulation tools" (a white hand) and then you can change distance and angle with it.
The "Translate by" allows you to translate the length of a bond into the new position via X, Y, and Z, and the "Rotate around" allows you to rotate your selection around current geometry or origin.
finally, if you want to undo your adjustments select on the "Edit in the toolbar" and select "Undo manipulate atom".
On the other hand, you can use GaussView instead of Avogadro, bacause you can change angles and bonds with select on "Modify angle" and "Modify bond". I think it's easier and more accurate to use GaussView to make these changes.
Best,
Tahereh
Hi!
I would suggest you to use another software if you want to manipulate manually your adsorbates e.g. VMD. Personally I only use avogadro to build crystals or big cells with gas-phase molecules, but not for adsoption slabs.
Instead, VMD is a really nice tool (and its opens source too), that allows you to move and rotate your adsorbates very easy. Here you can find all the information, manuals, and everything you need to know about it: https://www.ks.uiuc.edu/Research/vmd/
Additionally if you are using a benchmark software to perform DFT (like VASP) you dont need to convert the output files to an xyz to visualize it, and you can also set the renderization parameters to export fancy images.
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